Christian Brander1 and Bruce D. Walker2
1AIDS Research Center, Massachusetts General Hospital, 149 13th Street, Room 5234,
2Charlestown, MA 02129, USA, and Harvard Medical School Boston, MA USA
Updated October 1997
Characterization of the cellular immune response against HIV has led to the identification of numerous HLA class I restricted CTL epitopes and many laboratories have contributed to the description of CTL epitopes in most of the HIV-1 proteins. Since the last update of this CTL epitope list in 1996, a number of new epitopes have been published and are included in the current update. References have also been updated for epitopes previously listed as personal communications which have since been published.
For this update, we maintained the same rigid criteria for inclusion in the list of optimal epitopes as in previous years. First, the peptide has to be involved in the natural immune response against HIV. Thus, only epitopes that have been shown to induce a specific CTL response upon HIV infection in vivo are included. Second, the peptides have to be truncated to the size of the optimal epitope, which is the shortest epitope that is recognized at the lowest peptide concentration; and third, the HLA class I restricting molecule has to be identified. We therefore excluded epitopes from the list of optimal epitopes if only the binding to a certain class I molecule has been shown but not the immunogenicity in vivo, or if no peptide titration assay with truncated peptides has been reported. However, those epitopes are included in the extended CTL epitope list in Part-I of this database. Nine newly listed optimal epitopes are included this year, bringing the total number to 110. These epitopes add to the previously identified pattern of CTL epitopes being widely distributed over the expressed HIV proteins.
In order to keep this list updated it would be very helpful for us to receive information about newly identified epitopes as they become available. For comments and/or contributions to this CTL epitope list (C.B. or B.W.) or the main database (B.K.) please call, write, or mail us at:
Bette Korber Christian Brander Bruce D. Walker phone: 505 665 4453 phone: 617 724 5789 phone: 617 724 8332 FAX: 505 665 3493 FAX: 617 726 5411 FAX: 617 726 4691 btk@t10.lanl.gov Brander@Helix.MGH.Harvard.Edu BWalker@Helix.MGH.Harvard.Edu Table-1 Best Defined HIV CTL Epitopes HLA Protein AA Isolate Sequence Reference HLA-A2 2 C Falk91 L V I L p17 77-85 LAI SLYNTVATL Johnson91,Parker92,Parker94 RT 346-354 LAI VIYQYMDDL Harrer96 RT 476-484 LAI ILKEPVHGV Walker89,Tsomides91 A*0201 gp120 311-320 IIIB RGPGRAFVTI Alexander-Miller96 gp41 818-827 LAI SLLNATDIAV Dupuis95 nef 136-145 LAI PLTFGWCYKL Haas96, B. Maier and B. Autran Per.comm. nef 180-189 LAI VLEWRFDSRL Haas96, B. Maier and B. Autran Per.comm. nef 190-198 LAI AFHHVAREL Hadida95, B. Autran Per.comm. HLA-A3.1 23 C DiBrino93 IF K L Y p17 18-26 LAI KIRLRPGGK Harrer96b p17 20-28 LAI RLRPGGKKK B. Culmann, D. Lewinsohn, D. Ruhl, S. Riddell, B. Wilkes, Per.comm.,Goulder97 p17 20-29 LAI RLRPGGKKKY B. Wilkes, D. Ruhl Per.comm. RT 325-333 LAI AIFQSSMTK Threlkeld97 gp120 37-46 LAI TVYYGVPVWK Johnson94 gp41 775-785 LAI RLRDLLLIVTR Takahashi91 nef 73-82 LAI QVPLRPMTYK Koenig90,Culmann91 HLA-A11 2 C Zhang93 I K L p17 84-92 LAI TLYCVHQRI T. Harrer Per.comm. p24 349-359 III-B ACQGVGGPGGHK Sipsas97 RT 325-333 LAI AIFQSSMTK Johnson94b,Zhang93,Threlkeld97 RT 508-517 LAI IYQEPFKNLK B. Culmann Per.comm. nef 73-82 LAI PLRPMTYK Culmann91 nef 84-92 LAI AVDLSHFLK Culmann91 HLA-A19 A*7401 RT 71-79 Clade A/B/D ITLWQRPLV S. Rowland-Jones Per.comm. HLA-A24 p17 28-36 LAI KYKLKHIVW D. Lewinsohn Per.comm. gp120 53-62 LAI LFCASDAKAY Lieberman92,Shankar96 gp41 591-598 LAI YLKDQQLL Dai92 HLA-A25 p24 145-155 LAI QAISPRTLNAW I. Kurane, K. West Per.comm. p24 203-212 LAI ETINEEAAEW Klenerman96,vanBaalen96 HLA-A26 p24 167-175 LAI EVIPMFSAL Goulder96b RT 593-603 LAI ETFYVDGAANR B. Wilkes, D. Ruhl Per.comm. HLA-A28 A*6802 RT 71-79 Clade A/B/D ITLWQRPLV S. Rowland-Jones Per.comm. A*6802 RT 85-93 Clade D DTVLEEMNL S. Rowland-Jones Per.comm. HLA-A29 gp120 376-384 LAI FNCGGEFFY Wilson97 HLA-A31 gp41 775-785 LAI RLRDLLLIVTR Safrit94a,Safrit94b HLA-A32 RT 559-568 LAI PIQKETWETW Harrer96b gp120 419-427 HXB2 RIKQIINMW Harrer96b HLA-B7 123 C Englehard93 APR L p24 148-156 LAI SPRTLNAWV D. Lewinsohn Per.comm. p24 179-187 LAI ATPQDLNTM B. Wilkes, D. Ruhl Per.comm. RT 323-332 LAI SPAIFQSSMT C. Hey and D. Ruhl, Per.comm. gp120 303-312 LAI RPNNNTRKSI Safrit94b gp41 843-851 LAI IPRRIRQGL B. Wilkes and D. Ruhl, Per.comm. nef 68-77 LAI FPVTPQVPLR Haas96, B. Maier and B. Autran Per.comm. nef 77-85 LAI RPMTYKAAL Bauer97 nef 128-137 LAI TPGPGVRYPL CulmannPenciolelli94,Haas96, B. Maier and B. Autran Per.comm. HLA-B8 23 5 C Hill92b,Sutton93 P R L LK K I M p17 24-31 LAI GGKKKYKL RowlandJones93a,Goulder97 p17 74-82 LAI ELRSLYNTV Goulder97c p24 259-267 LAI EIYKRWII Sutton93,Goulder97c gp120 2-10 III-B RVKEKYQHL Sipsas97 gp41 591-598 LAI YLKDQQLL Johnson92,Shankar96 nef 13-20 LAI WPTVRERM Goulder97c nef 90-97 LAI FLKEKGGL CulmannPenciolelli94,Price97 HLA-B14 23 56 C DiBrino94b RL RI L KY HL F p24 183-191 LAI DLNTMLNTV Nixon88b,Johnson92 p24 298-306 LAI DRFYKTLRA Harrer96b gp41 589-597 LAI ERYLKDQQL Johnson92 HLA-B15 gp120 375-383 LAI SFNCGGEFF Wilson97 HLA-B18 nef 135-143 LAI YPLTFGWCY Culmann91,CulmannPenciolelli94 HLA-B27 2 C Jardetzky91 R K R p17 18-27 LAI KIRLRPGGKK D. Lewinsohn Per.comm. p17 19-27 LAI IRLRPGGKK D. Lewinsohn Per.comm. p24 263-272 LAI KRWIILGLNK Nixon88,Buseyne93 gp41 590-597 LAI RYLKDQQL Shankar96 gp41 791-799 LAI GRRGWEALKY Lieberman92, J. Lieberman Per.comm. B*2703 gag 260-269 HIV-2 RRWIQLGLQK S. Rowland-Jones Per.comm. B*2705 nef 105-114 LAI RRQDILDLWI Goulder97d nef 73-82 LAI QVPLRPMTYK B. Culmann Per.comm. nef 134-141 LAI RYPLTFGW B. Culmann Per.comm. HLA-B35 2 C Hill92b P Y S p17 124-132 LAI NSSKVSQNY RowlandJones95 p17 36-44 LAI WASRELERF Goulder97a p24 254-262 LAI PPIPVGDIY RowlandJones95 RT 262-270 LAI TVLDVGDAY B. Wilkes, D. Ruhl Per.comm. RT 273-282 III-B VPLDEDFRKY Sipsas97,Shiga96 RT 328-336 III-B NPDIVIYQY Sipsas97,Shiga96 RT 342-350 LAI HPDIVIYQY RowlandJones95 gp120 42-52 LAI VPVWKEATTTL B. Wilkes, D. Ruhl Per.comm. gp41 611-619 LAI TAVPWNASW Johnson94 nef 74-81 LAI VPLRPMTY Culmann91,CulmannPenciolelli94 gag 245-253 HIV-2 NPVPVGNIY RowlandJones95 HLA-B37 nef 120-128 LAI YFPDWQNYT Culmann91 and Per.comm. HLA-B39 p24 193-201 LAI GHQAAMQML I. Kurane, K. West Per.comm. HLA-B42 p17 20-29 LAI RLRPGGKKKY B. Wilkes, D. Ruhl Per.comm. RT 438-446 LAI YPGIKVRQL B. Wilkes, D. Ruhl Per.comm. HLA-B44 p24 306-316 LAI AEQASQDVKNW Lewinsohn Per.comm. gp120 30-38 LAI AENLWVTVY Borrow97 HLA-B45 RT 591-600 LAI GAETFYVDGA B. Wilkes, D. Ruhl Per.comm. HLA-B51 p24 325-333 LAI NANPDCKTI B. Wilkes, D. Ruhl Per.comm. RT 295-302 III-B TAFTIPSI Sipsas97 gp41 557-565 III-B RAIEAQQHL Sipsas97 HLA-B52 p24 275-282 LAI RMYSPTSI B. Wilkes, D. Ruhl Per.comm. HLA-B53 2 C Hill92b P Y F W HIV-2 gag 173-181 HIV-2 TPYDINQML Gotch93 HLA-B55 gp120 42-51 LAI VPVWKEATTT Shankar96 HLA-B57 p24 147-155 III-B ISPRTLNAW Johnson91,Goulder96 p24 140-149 LAI TSTLQEQIGW Goulder96 p24 162-172 LAI KAFSPEVIPMF Goulder96 p24 240-249 LAI TSTLQEQIGW Goulder96 p24 311-319 LAI QASQEVKNW Goulder96 p24 311-319 LAI QASQDVKNW Goulder96 nef 116-125 LAI HTQGYFPDWQ Culmann91 nef 120-128 LAI YFPDWQNYT Culmann91 HLA-B58 p24 240-249 LAI TSTLQEQIGW Goulder96 HLA-B60 p17 93-101 LAI EIKDTKEAL A. Trocha and S. Kalams Per.comm. HLA-Bw62 p17 20-29 LAI RLRPGGKKKY Johnson91, B. Wilkes, D. Ruhl Per.comm. p24 268-277 LAI LGLNKIVRMY Johnson91 RT 415-426 III-B LVGKLNWASQIY P. Johnson Per.comm. RT 476-485 LAI ILKEPVHGVY Johnson91, P. Johnson Per.comm. nef 84-91 LAI AVDLSHFL CulmannPenciolelli94 nef 117-127 LAI TQGYFPDWQNY B. Culmann Per.comm. HLA-Cw*01,02 p24 168-175 LAI VIPMFSAL P. Goulder in press AIDS HLA-Cw4 2 C Falk94 Y F P L F M gp120 380-388 LAI SFNCGGEFF Johnson93,Wilson97 C*0401 p24 308-316 LAI QASQEVKNW Buseyne97
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